@article{2f65e684ede04114897fea40f29366c2,
title = "Analysis of estrogen-regulated enhancer RNAs identifies a functional motif required for enhancer assembly and gene expression",
abstract = "To better understand the functions of non-coding enhancer RNAs (eRNAs), we annotated the estrogen-regulated eRNA transcriptome in estrogen receptor α (ERα)-positive breast cancer cells using PRO-cap and RNA sequencing. We then cloned a subset of the eRNAs identified, fused them to single guide RNAs, and targeted them to their ERα enhancers of origin using CRISPR/dCas9. Some of the eRNAs tested modulated the expression of cognate, but not heterologous, target genes after estrogen treatment by increasing ERα recruitment and stimulating p300-catalyzed H3K27 acetylation at the enhancer. We identified a ∼40 nucleotide functional eRNA regulatory motif (FERM) present in many eRNAs that was necessary and sufficient to modulate gene expression, but not the specificity of activation, after estrogen treatment. The FERM interacted with BCAS2, an RNA-binding protein amplified in breast cancers. The ectopic expression of a targeted eRNA controlling the expression of an oncogene resulted in increased cell proliferation, demonstrating the regulatory potential of eRNAs in breast cancer.",
keywords = "Breast cancer, CP: Molecular biology, H3K27 acetylation, coregulator, enhancer, enhancer RNA (eRNA), estrogen receptor alpha (ERα), noncoding RNA, p300/CBP, pre-mRNA-splicing factor (SPF27/BCAS2), transcription",
author = "Hou, {Tim Y.} and Kraus, {W. Lee}",
note = "Funding Information: The authors thank the members of the Kraus lab for helpful feedback on this work, especially Shino Murakami, Rebecca Gupte, Aarin Jones, Andrea Edwards, Cristel Camacho, and David Owen; the members of the Green Center for Reproductive Biology Sciences Computational Core Facility for assistance with data analysis; Dr. Gary Hon and Dr. Shiqi Xie (University of Texas Southwestern Medical Center, Dallas) for helpful discussions and the dCas9-Flag construct; Rebecca Gupte for the purified p300; and Shu-Ping Chiu for assistance with the 6xHIs-BCAS2 purification. The also acknowledge the following core facilities at University of Texas Southwestern Medical Center: the McDermott Center Next Generation Sequencing Core (Dr. Ralf Kittler and Vanessa Schmid) and the UT Southwestern Proteomics Core (Dr. Andrew Lemoff). The breast cancer datasets used for the analyses described in this manuscript were obtained from dbGaP at www.ncbi.nlm.nih.gov/gap through dbGaP accession number phs000676. This work was supported by a grant from the NIH/NIDDK (R01 DK058110), grants from the Cancer Prevention and Research Institute of Texas (CPRIT; RP160318 and RP190235), and funds from the Cecil H. and Ida Green Center for Reproductive Biology Sciences Endowment to W.L.K. T.Y.H. and W.L.K. conceived the project, designed the experiments, oversaw their execution, and analyzed the data. T.Y.H. performed all the experiments and data analysis. T.Y.H. prepared the initial drafts of the figures and text, which were edited and finalized by W.L.K. W.L.K. secured funding for the work and provided overall project direction. The authors declare no competing interests. Funding Information: The authors thank the members of the Kraus lab for helpful feedback on this work, especially Shino Murakami, Rebecca Gupte, Aarin Jones, Andrea Edwards, Cristel Camacho, and David Owen; the members of the Green Center for Reproductive Biology Sciences Computational Core Facility for assistance with data analysis; Dr. Gary Hon and Dr. Shiqi Xie (University of Texas Southwestern Medical Center, Dallas) for helpful discussions and the dCas9-Flag construct; Rebecca Gupte for the purified p300; and Shu-Ping Chiu for assistance with the 6xHIs-BCAS2 purification. The also acknowledge the following core facilities at University of Texas Southwestern Medical Center: the McDermott Center Next Generation Sequencing Core (Dr. Ralf Kittler and Vanessa Schmid) and the UT Southwestern Proteomics Core (Dr. Andrew Lemoff). The breast cancer datasets used for the analyses described in this manuscript were obtained from dbGaP at www.ncbi.nlm.nih.gov/gap through dbGaP accession number phs000676. This work was supported by a grant from the NIH / NIDDK ( R01 DK058110 ), grants from the Cancer Prevention and Research Institute of Texas ( CPRIT ; RP160318 and RP190235 ), and funds from the Cecil H. and Ida Green Center for Reproductive Biology Sciences Endowment to W.L.K. Publisher Copyright: {\textcopyright} 2022 The Author(s)",
year = "2022",
month = jun,
day = "14",
doi = "10.1016/j.celrep.2022.110944",
language = "English (US)",
volume = "39",
journal = "Cell Reports",
issn = "2211-1247",
publisher = "Cell Press",
number = "11",
}